Modulome

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.11

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Modulome
        Analysis of public microbial RNA-seq data

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Contact E-mail
        avsastry@ucsd.edu
        Application Type
        Microbial RNA-seq Analysis

        Report generated on 2023-02-14, 08:13 based on data in: /tmp/nxf.Y7NSFpiaNO


        General Statistics

        Showing 338/338 rows and 9/10 columns.
        Sample Name% AssignedM Assigned% AlignedM Aligned% BP Trimmed% Dups% GCLengthM Seqs
        DRX300641
        1.8%
        0.4
        87.1%
        21.2
        8.0%
        94.0%
        50%
        35 bp
        24.3
        DRX300642
        1.4%
        0.4
        87.6%
        27.9
        7.1%
        95.2%
        50%
        35 bp
        31.8
        DRX300643
        1.8%
        0.5
        87.1%
        22.5
        7.1%
        94.1%
        50%
        35 bp
        25.9
        ERX1222798
        2.3%
        0.3
        97.6%
        12.3
        4.3%
        94.8%
        50%
        35 bp
        12.6
        ERX1222799
        1.5%
        0.2
        98.1%
        12.0
        7.9%
        95.7%
        50%
        35 bp
        12.3
        ERX1222800
        1.9%
        0.2
        98.1%
        9.7
        3.9%
        94.8%
        50%
        36 bp
        9.9
        ERX2826862
        4.6%
        1.1
        98.0%
        23.1
        2.9%
        95.2%
        50%
        36 bp
        23.6
        ERX2826863
        4.9%
        1.0
        98.0%
        20.0
        2.9%
        94.7%
        50%
        36 bp
        20.5
        ERX2826864
        4.6%
        1.6
        97.7%
        33.8
        3.8%
        95.5%
        50%
        36 bp
        34.6
        ERX2826865
        5.4%
        0.8
        98.0%
        15.3
        3.0%
        94.1%
        50%
        36 bp
        15.6
        ERX2826866
        5.4%
        1.6
        97.8%
        29.2
        3.8%
        95.4%
        50%
        36 bp
        29.8
        ERX2826867
        5.2%
        1.2
        98.1%
        21.6
        3.6%
        95.3%
        50%
        36 bp
        22.1
        ERX2826868
        4.5%
        1.4
        98.0%
        31.1
        3.3%
        95.9%
        50%
        36 bp
        31.7
        ERX2826869
        4.4%
        0.5
        98.2%
        11.4
        2.6%
        94.2%
        50%
        36 bp
        11.6
        ERX2826870
        4.2%
        1.0
        98.0%
        23.1
        2.8%
        95.4%
        50%
        36 bp
        23.6
        ERX4581838
        4.7%
        1.0
        98.0%
        20.1
        2.8%
        94.9%
        50%
        36 bp
        20.5
        ERX4581839
        4.6%
        0.7
        98.7%
        16.0
        2.1%
        95.9%
        50%
        36 bp
        16.2
        ERX4581840
        4.9%
        0.8
        98.7%
        16.6
        2.0%
        95.7%
        50%
        36 bp
        16.8
        ERX4581841
        2.9%
        1.3
        79.5%
        36.3
        8.4%
        86.7%
        49%
        35 bp
        45.7
        ERX4581842
        3.1%
        0.5
        80.6%
        13.6
        7.1%
        83.9%
        49%
        35 bp
        16.8
        ERX4581843
        3.3%
        0.7
        81.1%
        17.5
        6.8%
        85.3%
        49%
        35 bp
        21.6
        ERX4581844
        3.1%
        1.1
        80.1%
        28.5
        8.3%
        86.8%
        49%
        35 bp
        35.6
        ERX4581845
        3.2%
        0.5
        82.2%
        13.1
        5.8%
        84.5%
        49%
        35 bp
        15.9
        ERX4581846
        2.8%
        0.5
        81.7%
        15.6
        6.5%
        85.7%
        49%
        35 bp
        19.1
        ERX4581847
        4.2%
        0.9
        98.5%
        20.2
        3.5%
        96.1%
        50%
        36 bp
        20.5
        ERX4581848
        4.7%
        0.7
        98.6%
        15.7
        2.9%
        95.6%
        50%
        36 bp
        15.9
        ERX4581849
        4.4%
        0.8
        97.3%
        18.9
        4.3%
        95.1%
        50%
        36 bp
        19.4
        ERX4581850
        5.1%
        0.9
        98.0%
        18.0
        2.7%
        95.1%
        50%
        36 bp
        18.4
        ERX4581851
        4.6%
        0.9
        97.6%
        19.7
        3.3%
        95.2%
        50%
        36 bp
        20.2
        ERX4581852
        4.8%
        0.8
        98.0%
        16.5
        2.6%
        95.2%
        50%
        36 bp
        16.8
        ERX4581853
        4.6%
        1.0
        97.4%
        20.7
        4.2%
        93.8%
        49%
        36 bp
        21.2
        ERX4581854
        3.9%
        1.1
        97.6%
        26.5
        3.6%
        94.6%
        50%
        36 bp
        27.1
        ERX4581855
        4.4%
        1.0
        97.6%
        21.8
        4.0%
        94.7%
        49%
        36 bp
        22.3
        ERX4581856
        5.0%
        1.9
        97.4%
        37.3
        4.6%
        95.0%
        49%
        36 bp
        38.3
        ERX4581857
        4.5%
        1.0
        97.9%
        20.8
        3.2%
        94.7%
        49%
        36 bp
        21.3
        ERX4581858
        5.0%
        1.2
        97.8%
        24.3
        3.3%
        94.6%
        49%
        36 bp
        24.8
        ERX4581859
        4.9%
        1.1
        97.8%
        21.8
        4.6%
        95.6%
        50%
        36 bp
        22.3
        ERX4581860
        4.1%
        0.9
        97.7%
        21.0
        5.7%
        96.0%
        50%
        36 bp
        21.5
        ERX4581861
        5.2%
        1.6
        97.8%
        30.0
        4.9%
        96.1%
        50%
        36 bp
        30.7
        ERX4597138
        5.3%
        1.1
        98.4%
        21.3
        3.4%
        95.6%
        50%
        36 bp
        21.6
        ERX4597139
        5.3%
        1.3
        98.2%
        23.6
        3.3%
        95.8%
        50%
        36 bp
        24.1
        ERX4597140
        5.2%
        1.2
        97.9%
        21.6
        4.5%
        95.5%
        50%
        36 bp
        22.0
        ERX4651385
        4.3%
        0.8
        98.1%
        18.1
        3.0%
        95.8%
        50%
        36 bp
        18.4
        ERX4651386
        4.4%
        0.9
        98.4%
        19.0
        2.8%
        95.6%
        50%
        36 bp
        19.3
        ERX4651387
        5.3%
        1.4
        98.2%
        26.6
        2.7%
        95.9%
        50%
        36 bp
        27.1
        ERX4663691
        4.6%
        0.9
        98.1%
        19.3
        2.8%
        95.5%
        50%
        36 bp
        19.7
        ERX4663692
        4.4%
        1.3
        95.8%
        28.6
        3.8%
        95.3%
        50%
        35 bp
        29.8
        ERX5310346
        4.5%
        0.7
        95.8%
        15.2
        4.1%
        94.0%
        50%
        35 bp
        15.9
        ERX5311170
        4.9%
        0.7
        95.1%
        13.9
        6.0%
        93.3%
        50%
        35 bp
        14.6
        ERX5311171
        4.4%
        1.3
        95.5%
        29.0
        4.3%
        94.9%
        50%
        35 bp
        30.3
        ERX5311172
        4.4%
        0.7
        95.6%
        14.5
        4.3%
        93.7%
        49%
        35 bp
        15.1
        ERX7722950
        4.2%
        0.6
        96.2%
        13.6
        3.5%
        94.1%
        49%
        35 bp
        14.1
        ERX7722951
        4.7%
        1.9
        95.5%
        37.7
        4.3%
        95.2%
        49%
        35 bp
        39.5
        ERX7722952
        4.2%
        0.7
        95.8%
        14.8
        3.8%
        93.2%
        50%
        35 bp
        15.4
        ERX7722953
        4.3%
        0.9
        95.7%
        19.6
        4.4%
        94.5%
        49%
        35 bp
        20.5
        ERX7722954
        4.4%
        0.8
        95.7%
        17.2
        4.0%
        94.2%
        49%
        35 bp
        18.0
        ERX7722955
        4.9%
        1.0
        95.6%
        20.2
        4.0%
        94.0%
        50%
        35 bp
        21.1
        SRX10063114
        10.4%
        1.7
        91.1%
        14.9
        3.2%
        90.2%
        46%
        147 bp
        16.4
        SRX10063115
        8.9%
        1.0
        91.3%
        10.7
        2.6%
        89.3%
        47%
        148 bp
        11.7
        SRX10063116
        9.0%
        2.1
        91.7%
        21.3
        3.2%
        92.0%
        46%
        147 bp
        23.2
        SRX10063117
        48.4%
        0.2
        63.7%
        0.3
        0.9%
        41.8%
        34%
        271 bp
        0.5
        SRX10063118
        41.8%
        0.3
        61.2%
        0.4
        0.9%
        51.9%
        34%
        286 bp
        0.6
        SRX10063119
        45.9%
        0.2
        61.1%
        0.3
        4.9%
        46.1%
        35%
        282 bp
        0.5
        SRX10828555
        35.9%
        0.1
        58.3%
        0.2
        1.0%
        42.0%
        34%
        288 bp
        0.3
        SRX10828556
        52.9%
        0.4
        65.1%
        0.4
        0.8%
        48.4%
        35%
        262 bp
        0.7
        SRX10828557
        54.8%
        0.5
        67.6%
        0.6
        3.8%
        52.9%
        34%
        264 bp
        0.9
        SRX10828558
        47.2%
        0.3
        63.0%
        0.4
        0.8%
        50.0%
        33%
        270 bp
        0.7
        SRX10828559
        38.4%
        0.2
        55.0%
        0.3
        5.5%
        52.8%
        36%
        276 bp
        0.6
        SRX10828560
        40.1%
        0.2
        57.4%
        0.2
        0.9%
        45.9%
        34%
        288 bp
        0.4
        SRX10828561
        38.5%
        0.1
        59.2%
        0.2
        5.3%
        44.6%
        34%
        284 bp
        0.3
        SRX10828562
        46.5%
        0.2
        63.3%
        0.3
        0.8%
        49.2%
        35%
        271 bp
        0.5
        SRX10828563
        52.5%
        0.6
        67.2%
        0.8
        0.7%
        58.1%
        34%
        269 bp
        1.2
        SRX10828564
        78.8%
        18.1
        90.0%
        20.7
        1.8%
        90.4%
        36%
        98 bp
        22.9
        SRX10828565
        79.3%
        18.1
        89.8%
        20.5
        1.8%
        90.5%
        35%
        98 bp
        22.9
        SRX10828566
        78.2%
        17.9
        89.6%
        20.5
        1.9%
        90.0%
        35%
        98 bp
        22.8
        SRX12529174
        79.3%
        17.0
        90.4%
        19.4
        2.0%
        89.4%
        36%
        98 bp
        21.4
        SRX12529175
        79.8%
        17.8
        90.7%
        20.2
        1.7%
        89.8%
        35%
        99 bp
        22.3
        SRX13365952
        80.3%
        17.7
        91.5%
        20.1
        2.1%
        90.2%
        36%
        98 bp
        22.0
        SRX13365953
        79.2%
        18.8
        90.4%
        21.4
        1.7%
        90.3%
        36%
        99 bp
        23.7
        SRX13365954
        77.0%
        5.0
        92.7%
        6.1
        7.8%
        74.0%
        35%
        138 bp
        6.6
        SRX13376825
        79.4%
        6.7
        92.7%
        7.8
        5.5%
        74.9%
        35%
        141 bp
        8.4
        SRX13376826
        79.0%
        5.6
        93.3%
        6.6
        8.4%
        88.0%
        35%
        138 bp
        7.1
        SRX13376827
        0.6%
        0.6
        0.9%
        1.0
        2.1%
        74.4%
        51%
        35 bp
        107.1
        SRX13376828
        0.2%
        0.2
        1.2%
        1.2
        2.2%
        72.5%
        51%
        35 bp
        96.2
        SRX13376829
        0.2%
        0.1
        0.3%
        0.3
        2.0%
        75.0%
        51%
        35 bp
        91.6
        SRX13376831
        0.2%
        0.2
        0.4%
        0.4
        2.8%
        50.2%
        47%
        85 bp
        98.2
        SRX13376834
        0.2%
        0.1
        0.4%
        0.3
        5.0%
        67.6%
        54%
        92 bp
        87.4
        SRX13376835
        0.3%
        0.3
        0.4%
        0.5
        3.0%
        67.9%
        50%
        102 bp
        106.1
        SRX13376836
        2.9%
        1.5
        99.5%
        51.3
        1.2%
        97.9%
        51%
        36 bp
        51.5
        SRX13376837
        2.9%
        1.0
        99.5%
        34.0
        1.1%
        98.0%
        51%
        36 bp
        34.1
        SRX13376838
        2.8%
        1.4
        99.5%
        50.3
        1.2%
        98.2%
        51%
        36 bp
        50.5
        SRX13376839
        3.4%
        1.2
        99.4%
        35.2
        1.2%
        97.3%
        50%
        36 bp
        35.4
        SRX13376840
        3.1%
        1.4
        97.2%
        44.4
        2.9%
        98.2%
        51%
        36 bp
        45.8
        SRX13376841
        3.3%
        1.4
        99.4%
        43.5
        1.3%
        97.9%
        51%
        36 bp
        43.8
        SRX13376842
        46.9%
        11.3
        92.2%
        22.3
        1.0%
        91.1%
        38%
        50 bp
        24.1
        SRX13376843
        63.7%
        14.9
        91.5%
        21.5
        1.0%
        90.0%
        36%
        50 bp
        23.5
        SRX13376844
        65.3%
        16.0
        91.2%
        22.4
        1.0%
        88.7%
        36%
        50 bp
        24.6
        SRX13376845
        64.9%
        14.8
        92.4%
        21.0
        1.0%
        89.6%
        36%
        50 bp
        22.8
        SRX13376846
        45.7%
        11.7
        92.5%
        23.7
        1.0%
        90.8%
        38%
        50 bp
        25.6
        SRX13376847
        46.0%
        11.8
        92.5%
        23.6
        1.0%
        90.7%
        38%
        50 bp
        25.6
        SRX13376848
        65.2%
        17.1
        89.3%
        23.5
        1.0%
        89.2%
        36%
        50 bp
        26.3
        SRX13376849
        54.4%
        13.1
        91.4%
        22.0
        1.0%
        90.2%
        37%
        50 bp
        24.1
        SRX13376850
        54.9%
        15.5
        91.6%
        25.8
        1.0%
        90.7%
        37%
        50 bp
        28.2
        SRX13376851
        55.4%
        14.7
        91.8%
        24.3
        1.0%
        90.5%
        37%
        50 bp
        26.5
        SRX13376852
        55.5%
        14.2
        91.6%
        23.4
        1.0%
        90.6%
        37%
        50 bp
        25.5
        SRX13376853
        59.5%
        12.1
        91.5%
        18.6
        1.0%
        89.3%
        36%
        50 bp
        20.4
        SRX13376854
        29.1%
        10.3
        99.3%
        35.1
        1.3%
        95.6%
        44%
        50 bp
        35.4
        SRX13376855
        32.6%
        11.2
        99.2%
        34.1
        1.0%
        95.0%
        44%
        50 bp
        34.4
        SRX13376856
        26.4%
        6.1
        98.7%
        22.9
        0.3%
        95.2%
        44%
        51 bp
        23.2
        SRX13376857
        25.5%
        7.1
        99.2%
        27.6
        0.9%
        95.3%
        44%
        51 bp
        27.9
        SRX13376858
        26.6%
        6.4
        99.3%
        23.9
        1.3%
        94.8%
        44%
        50 bp
        24.1
        SRX13376859
        30.3%
        6.8
        98.8%
        22.0
        0.5%
        94.7%
        43%
        51 bp
        22.3
        SRX13376860
        73.2%
        12.6
        87.1%
        15.0
        3.8%
        76.0%
        34%
        98 bp
        17.2
        SRX13376861
        73.0%
        12.1
        87.3%
        14.5
        2.5%
        78.6%
        35%
        97 bp
        16.6
        SRX13376862
        73.5%
        8.3
        86.3%
        9.8
        2.7%
        78.9%
        35%
        97 bp
        11.3
        SRX13376863
        76.4%
        10.4
        86.2%
        11.7
        3.8%
        78.3%
        34%
        97 bp
        13.6
        SRX13376864
        64.5%
        7.6
        84.1%
        9.8
        2.7%
        68.7%
        33%
        98 bp
        11.7
        SRX13376865
        73.2%
        11.1
        84.6%
        12.8
        2.7%
        72.7%
        33%
        98 bp
        15.1
        SRX13376866
        71.4%
        5.1
        93.8%
        6.7
        0.1%
        83.2%
        35%
        51 bp
        7.2
        SRX13827967
        62.0%
        4.5
        84.2%
        6.2
        0.1%
        82.2%
        37%
        51 bp
        7.3
        SRX13827968
        71.1%
        2.3
        91.7%
        2.9
        0.2%
        66.8%
        34%
        74 bp
        3.2
        SRX13827969
        73.5%
        3.0
        89.4%
        3.6
        0.1%
        71.2%
        34%
        74 bp
        4.0
        SRX13827970
        73.6%
        3.3
        91.4%
        4.0
        0.1%
        70.8%
        34%
        74 bp
        4.4
        SRX14043139
        71.3%
        3.1
        88.8%
        3.9
        0.1%
        70.2%
        34%
        74 bp
        4.4
        SRX14043140
        73.2%
        3.0
        89.3%
        3.6
        0.2%
        73.2%
        35%
        74 bp
        4.1
        SRX14043141
        74.4%
        5.2
        91.1%
        6.4
        0.1%
        76.7%
        34%
        74 bp
        7.0
        SRX14043142
        68.3%
        4.2
        85.6%
        5.3
        0.1%
        76.6%
        36%
        74 bp
        6.2
        SRX14043143
        54.3%
        1.9
        73.7%
        2.5
        0.2%
        67.4%
        38%
        74 bp
        3.4
        SRX14043144
        68.0%
        2.8
        90.5%
        3.7
        0.1%
        65.4%
        34%
        74 bp
        4.1
        SRX14468428
        68.6%
        3.0
        90.7%
        4.0
        0.1%
        68.8%
        34%
        74 bp
        4.4
        SRX14468429
        21.7%
        0.6
        24.3%
        0.7
        3.8%
        26.7%
        35%
        60 bp
        2.8
        SRX14468430
        21.5%
        1.1
        25.7%
        1.3
        3.2%
        39.1%
        35%
        53 bp
        5.2
        SRX14468431
        31.2%
        1.1
        35.3%
        1.2
        2.5%
        19.0%
        35%
        60 bp
        3.5
        SRX14468432
        44.6%
        1.9
        50.4%
        2.1
        2.7%
        23.8%
        36%
        59 bp
        4.2
        SRX14468433
        25.9%
        1.5
        29.3%
        1.7
        2.7%
        36.5%
        35%
        60 bp
        5.7
        SRX16159629
        14.7%
        0.4
        18.2%
        0.5
        3.1%
        32.9%
        34%
        53 bp
        2.7
        SRX16159630
        61.4%
        1.9
        69.0%
        2.1
        9.3%
        23.9%
        34%
        53 bp
        3.0
        SRX16159631
        43.5%
        1.1
        49.6%
        1.2
        2.9%
        22.8%
        34%
        53 bp
        2.5
        SRX16159632
        22.5%
        0.3
        26.7%
        0.3
        17.1%
        23.5%
        35%
        53 bp
        1.3
        SRX16159633
        18.3%
        0.3
        23.5%
        0.4
        4.5%
        31.5%
        35%
        53 bp
        1.9
        SRX16159634
        22.1%
        1.0
        26.0%
        1.2
        5.0%
        47.5%
        35%
        60 bp
        4.6
        SRX16159635
        39.5%
        1.3
        48.3%
        1.5
        7.7%
        36.8%
        37%
        59 bp
        3.2
        SRX16159636
        18.9%
        2.1
        24.1%
        2.7
        5.3%
        63.3%
        36%
        60 bp
        11.2
        SRX16159637
        12.7%
        0.5
        16.3%
        0.7
        6.3%
        45.1%
        36%
        60 bp
        4.2
        SRX1648205
        47.8%
        2.7
        54.4%
        3.1
        4.0%
        45.0%
        34%
        53 bp
        5.7
        SRX1648206
        38.6%
        1.9
        44.9%
        2.2
        3.4%
        41.4%
        34%
        59 bp
        4.8
        SRX1648207
        57.2%
        5.0
        65.6%
        5.7
        5.3%
        50.5%
        34%
        53 bp
        8.7
        SRX1648208
        21.3%
        1.5
        25.7%
        1.8
        3.1%
        50.2%
        35%
        53 bp
        7.0
        SRX1648209
        17.1%
        0.7
        19.9%
        0.8
        3.5%
        38.9%
        37%
        59 bp
        4.1
        SRX1648210
        43.6%
        2.6
        49.9%
        3.0
        3.2%
        41.1%
        34%
        53 bp
        6.0
        SRX1648211
        22.6%
        0.3
        26.8%
        0.3
        18.0%
        23.2%
        36%
        60 bp
        1.2
        SRX1648212
        18.3%
        0.3
        23.5%
        0.4
        5.4%
        29.2%
        35%
        53 bp
        1.8
        SRX17761060
        22.1%
        1.0
        26.0%
        1.2
        5.5%
        44.5%
        34%
        53 bp
        4.5
        SRX17761061
        39.4%
        1.2
        48.2%
        1.5
        8.4%
        35.8%
        37%
        59 bp
        3.1
        SRX17761062
        18.8%
        2.0
        24.1%
        2.6
        5.6%
        58.7%
        35%
        53 bp
        10.8
        SRX17761063
        12.7%
        0.5
        16.4%
        0.7
        6.8%
        44.2%
        36%
        60 bp
        4.1
        SRX17761064
        47.8%
        2.7
        54.4%
        3.1
        4.0%
        45.9%
        35%
        55 bp
        5.6
        SRX17761065
        38.6%
        1.9
        44.9%
        2.2
        3.4%
        41.4%
        34%
        59 bp
        4.8
        SRX17761066
        57.2%
        5.0
        65.6%
        5.7
        2.9%
        50.2%
        34%
        53 bp
        8.7
        SRX17761067
        21.3%
        1.5
        25.7%
        1.8
        3.9%
        51.9%
        34%
        60 bp
        7.0
        SRX17761068
        16.9%
        0.7
        19.6%
        0.8
        3.7%
        40.5%
        34%
        53 bp
        4.1
        SRX17761069
        43.6%
        2.6
        49.9%
        3.0
        2.5%
        41.6%
        34%
        59 bp
        6.0
        SRX17761070
        21.9%
        0.7
        24.6%
        0.8
        3.9%
        30.5%
        35%
        60 bp
        3.2
        SRX17761071
        22.0%
        1.3
        26.3%
        1.6
        2.4%
        37.5%
        36%
        60 bp
        5.9
        SRX17761072
        31.5%
        1.3
        35.5%
        1.4
        2.3%
        26.1%
        35%
        60 bp
        4.0
        SRX17761073
        44.2%
        2.1
        49.8%
        2.4
        2.5%
        30.0%
        36%
        59 bp
        4.7
        SRX17761074
        26.3%
        1.7
        29.6%
        1.9
        2.5%
        36.2%
        35%
        59 bp
        6.4
        SRX17761075
        15.3%
        0.5
        18.8%
        0.6
        2.0%
        30.9%
        34%
        53 bp
        3.1
        SRX17761076
        60.6%
        2.1
        68.0%
        2.3
        2.3%
        23.0%
        34%
        53 bp
        3.4
        SRX17761077
        43.1%
        1.2
        49.1%
        1.4
        3.5%
        21.7%
        34%
        53 bp
        2.8
        SRX17761078
        11.1%
        0.1
        38.3%
        0.4
        2.0%
        40.7%
        38%
        74 bp
        1.0
        SRX17761079
        11.5%
        0.1
        39.7%
        0.3
        1.0%
        77.6%
        33%
        75 bp
        0.8
        SRX17761080
        9.7%
        0.1
        37.4%
        0.5
        0.8%
        34.5%
        36%
        74 bp
        1.3
        SRX17761081
        7.9%
        0.2
        34.3%
        0.9
        1.3%
        49.7%
        35%
        75 bp
        2.6
        SRX17761082
        12.6%
        0.2
        30.5%
        0.4
        0.8%
        38.6%
        36%
        74 bp
        1.3
        SRX17761083
        11.2%
        0.3
        31.2%
        0.8
        0.9%
        86.7%
        30%
        75 bp
        2.7
        SRX17761084
        12.2%
        0.1
        40.0%
        0.3
        1.0%
        31.9%
        38%
        74 bp
        0.8
        SRX17761085
        11.8%
        0.1
        43.7%
        0.4
        0.4%
        76.8%
        33%
        75 bp
        0.9
        SRX17761086
        79.8%
        4.2
        95.6%
        5.0
        0.8%
        80.2%
        39%
        75 bp
        5.3
        SRX17761087
        81.9%
        5.2
        95.5%
        6.1
        0.2%
        79.2%
        37%
        75 bp
        6.4
        SRX17761088
        78.7%
        3.3
        95.4%
        4.0
        0.2%
        79.5%
        37%
        75 bp
        4.2
        SRX17761089
        82.8%
        4.0
        96.0%
        4.7
        0.2%
        78.8%
        37%
        75 bp
        4.9
        SRX17761090
        80.6%
        5.7
        93.8%
        6.6
        0.2%
        77.3%
        35%
        75 bp
        7.0
        SRX17761091
        78.9%
        4.3
        94.5%
        5.1
        0.8%
        77.0%
        36%
        74 bp
        5.4
        SRX17761092
        82.6%
        6.4
        96.2%
        7.4
        0.4%
        82.8%
        37%
        75 bp
        7.7
        SRX17761093
        80.6%
        4.8
        95.8%
        5.7
        0.8%
        80.4%
        38%
        75 bp
        5.9
        SRX17761094
        73.6%
        9.2
        86.5%
        10.8
        1.5%
        74.8%
        33%
        123 bp
        12.5
        SRX17761095
        70.0%
        7.4
        85.3%
        9.1
        1.6%
        73.6%
        34%
        123 bp
        10.6
        SRX17833718
        72.1%
        8.0
        84.5%
        9.4
        1.7%
        73.0%
        34%
        122 bp
        11.1
        SRX17833719
        71.8%
        8.2
        83.5%
        9.5
        1.6%
        70.3%
        34%
        122 bp
        11.4
        SRX2656779
        71.7%
        7.6
        86.2%
        9.2
        0.7%
        73.9%
        33%
        123 bp
        10.6
        SRX2656780
        74.1%
        9.5
        85.8%
        11.0
        0.7%
        80.6%
        34%
        123 bp
        12.9
        SRX2656781
        22.7%
        2.5
        98.8%
        10.8
        0.5%
        86.3%
        45%
        73 bp
        10.9
        SRX2656782
        29.9%
        3.6
        98.7%
        11.8
        0.5%
        85.8%
        44%
        73 bp
        12.0
        SRX2656783
        25.8%
        3.1
        98.7%
        11.8
        0.5%
        85.9%
        45%
        73 bp
        12.0
        SRX2656784
        16.3%
        2.1
        98.4%
        12.5
        0.4%
        88.1%
        47%
        73 bp
        12.7
        SRX322986
        32.9%
        4.0
        96.4%
        11.6
        0.5%
        84.3%
        44%
        73 bp
        12.1
        SRX322987
        22.4%
        2.6
        97.2%
        11.3
        0.4%
        86.7%
        45%
        73 bp
        11.6
        SRX322988
        19.8%
        2.2
        95.4%
        10.8
        0.5%
        85.6%
        45%
        73 bp
        11.3
        SRX3283115
        26.5%
        3.3
        94.8%
        11.7
        0.4%
        85.3%
        44%
        73 bp
        12.3
        SRX3343295
        16.3%
        1.9
        96.1%
        11.1
        0.4%
        86.9%
        46%
        73 bp
        11.6
        SRX3343296
        26.8%
        3.0
        99.1%
        11.0
        0.4%
        86.3%
        45%
        73 bp
        11.1
        SRX3343297
        28.7%
        3.5
        99.0%
        12.0
        0.5%
        85.7%
        45%
        73 bp
        12.1
        SRX3343298
        28.9%
        2.3
        99.0%
        7.7
        0.5%
        83.8%
        45%
        73 bp
        7.8
        SRX3353470
        26.5%
        3.0
        99.0%
        11.2
        0.5%
        85.5%
        45%
        73 bp
        11.3
        SRX3353471
        29.3%
        3.7
        99.0%
        12.6
        0.5%
        85.8%
        45%
        73 bp
        12.7
        SRX3353472
        24.1%
        2.7
        99.0%
        11.0
        0.5%
        86.1%
        45%
        73 bp
        11.1
        SRX3353473
        20.8%
        2.6
        99.1%
        12.2
        0.5%
        87.5%
        46%
        73 bp
        12.3
        SRX3353474
        29.9%
        3.7
        98.9%
        12.4
        0.5%
        85.9%
        44%
        73 bp
        12.5
        SRX3353475
        18.9%
        2.3
        99.1%
        12.0
        0.4%
        87.9%
        46%
        73 bp
        12.1
        SRX3353476
        23.3%
        2.7
        99.1%
        11.6
        0.4%
        87.1%
        46%
        73 bp
        11.7
        SRX3353477
        25.8%
        3.4
        99.2%
        13.2
        0.2%
        86.7%
        45%
        72 bp
        13.3
        SRX3353478
        72.0%
        5.9
        85.9%
        7.1
        0.4%
        81.9%
        36%
        70 bp
        8.2
        SRX3353479
        71.9%
        6.0
        86.5%
        7.2
        0.1%
        82.5%
        36%
        70 bp
        8.3
        SRX3651446
        71.3%
        6.1
        85.7%
        7.4
        0.1%
        84.8%
        37%
        70 bp
        8.6
        SRX3651447
        70.3%
        6.4
        89.8%
        8.1
        0.1%
        84.3%
        37%
        70 bp
        9.0
        SRX3651448
        56.3%
        3.6
        74.0%
        4.7
        0.1%
        78.9%
        39%
        70 bp
        6.4
        SRX3651449
        59.9%
        8.5
        76.2%
        10.9
        0.3%
        84.2%
        39%
        74 bp
        14.2
        SRX3651450
        68.2%
        5.1
        92.1%
        6.9
        0.3%
        84.2%
        36%
        70 bp
        7.5
        SRX3651451
        53.9%
        6.2
        90.3%
        10.4
        0.5%
        84.1%
        38%
        70 bp
        11.6
        SRX3651452
        62.6%
        7.5
        88.8%
        10.7
        0.1%
        85.6%
        36%
        70 bp
        12.0
        SRX3651453
        68.3%
        4.7
        88.5%
        6.1
        0.4%
        79.2%
        36%
        70 bp
        6.9
        SRX3651454
        63.6%
        5.9
        84.7%
        7.9
        0.1%
        83.1%
        37%
        70 bp
        9.4
        SRX3651455
        59.2%
        6.4
        92.0%
        9.9
        0.4%
        85.9%
        38%
        70 bp
        10.7
        SRX3651456
        62.0%
        4.9
        90.1%
        7.1
        0.1%
        85.8%
        37%
        70 bp
        7.9
        SRX4965401
        63.9%
        4.0
        88.1%
        5.5
        0.1%
        79.7%
        36%
        70 bp
        6.3
        SRX4965403
        60.9%
        6.3
        84.7%
        8.8
        0.3%
        86.7%
        38%
        70 bp
        10.4
        SRX4965404
        65.0%
        4.5
        87.4%
        6.1
        0.1%
        80.7%
        36%
        70 bp
        7.0
        SRX4965405
        66.8%
        4.1
        86.7%
        5.3
        0.1%
        79.1%
        36%
        70 bp
        6.1
        SRX4965407
        4.7%
        0.0
        6.3%
        0.0
        2.7%
        51.7%
        33%
        74 bp
        0.5
        SRX4965408
        82.7%
        32.5
        99.5%
        39.1
        0.9%
        94.5%
        35%
        50 bp
        39.3
        SRX4965409
        83.7%
        38.2
        99.6%
        45.4
        0.9%
        94.9%
        35%
        50 bp
        45.6
        SRX4965411
        83.5%
        35.1
        99.6%
        41.9
        0.9%
        95.0%
        35%
        50 bp
        42.0
        SRX4965412
        79.2%
        36.2
        99.6%
        45.6
        0.9%
        95.5%
        34%
        50 bp
        45.7
        SRX5029493
        79.5%
        33.0
        99.6%
        41.3
        0.9%
        94.3%
        35%
        50 bp
        41.5
        SRX5029494
        82.8%
        36.6
        99.6%
        44.0
        0.9%
        95.0%
        35%
        50 bp
        44.2
        SRX5029495
        80.5%
        33.0
        99.6%
        40.8
        0.9%
        95.1%
        35%
        50 bp
        41.0
        SRX5029496
        77.6%
        31.8
        99.6%
        40.8
        0.9%
        94.8%
        34%
        50 bp
        41.0
        SRX5029497
        75.8%
        29.3
        99.5%
        38.4
        0.9%
        93.7%
        34%
        50 bp
        38.6
        SRX5029498
        44.3%
        7.0
        89.8%
        14.2
        1.0%
        89.6%
        40%
        99 bp
        15.8
        SRX5029499
        37.4%
        6.0
        88.9%
        14.3
        0.8%
        90.2%
        42%
        99 bp
        16.1
        SRX5029500
        72.5%
        11.3
        92.0%
        14.3
        1.0%
        87.4%
        37%
        99 bp
        15.6
        SRX5029501
        67.5%
        3.2
        87.6%
        4.1
        0.1%
        83.1%
        36%
        74 bp
        4.7
        SRX5029502
        71.5%
        2.1
        91.1%
        2.7
        0.0%
        71.8%
        34%
        74 bp
        3.0
        SRX529230
        71.8%
        2.8
        91.2%
        3.5
        0.0%
        73.8%
        34%
        74 bp
        3.9
        SRX529231
        77.6%
        2.9
        91.0%
        3.4
        0.0%
        80.6%
        36%
        74 bp
        3.7
        SRX529232
        77.7%
        2.7
        91.1%
        3.1
        0.0%
        80.7%
        35%
        74 bp
        3.4
        SRX529233
        78.5%
        2.8
        91.2%
        3.2
        0.0%
        73.6%
        34%
        74 bp
        3.5
        SRX529234
        25.4%
        4.1
        40.0%
        6.5
        1.5%
        91.6%
        37%
        98 bp
        16.2
        SRX529235
        26.9%
        4.5
        41.6%
        7.0
        1.9%
        91.4%
        38%
        98 bp
        16.9
        SRX529236
        22.6%
        4.5
        36.7%
        7.3
        1.9%
        92.6%
        38%
        98 bp
        19.9
        SRX529237
        28.1%
        4.1
        40.0%
        5.9
        1.9%
        91.8%
        38%
        98 bp
        14.7
        SRX529238
        21.9%
        3.1
        33.2%
        4.7
        1.9%
        92.5%
        38%
        98 bp
        14.1
        SRX529239
        34.5%
        4.0
        49.1%
        5.7
        1.7%
        92.0%
        38%
        98 bp
        11.7
        SRX529240
        24.4%
        3.7
        38.4%
        5.8
        2.0%
        92.0%
        38%
        98 bp
        15.2
        SRX529241
        18.8%
        2.7
        29.1%
        4.2
        1.7%
        93.1%
        39%
        98 bp
        14.5
        SRX5562272
        24.5%
        3.8
        37.6%
        5.9
        1.7%
        93.1%
        39%
        98 bp
        15.6
        SRX5562273
        26.5%
        4.3
        41.4%
        6.8
        1.6%
        91.4%
        38%
        98 bp
        16.4
        SRX5562274
        32.6%
        5.3
        48.8%
        8.0
        1.8%
        91.0%
        36%
        98 bp
        16.4
        SRX5562275
        28.2%
        4.3
        44.3%
        6.8
        1.8%
        91.9%
        37%
        98 bp
        15.4
        SRX7080612
        71.7%
        5.0
        94.8%
        6.6
        0.3%
        85.2%
        34%
        70 bp
        6.9
        SRX7080613
        71.8%
        6.2
        95.4%
        8.2
        0.2%
        84.4%
        34%
        70 bp
        8.6
        SRX7080614
        72.9%
        6.5
        94.3%
        8.4
        0.3%
        84.0%
        34%
        70 bp
        8.9
        SRX7080615
        76.7%
        5.6
        94.8%
        6.9
        0.2%
        82.8%
        34%
        70 bp
        7.3
        SRX7080616
        76.3%
        5.6
        95.0%
        7.0
        0.0%
        82.7%
        35%
        70 bp
        7.4
        SRX7080617
        75.4%
        5.9
        93.7%
        7.3
        0.3%
        82.2%
        34%
        70 bp
        7.8
        SRX7122764
        75.0%
        5.7
        94.8%
        7.2
        0.2%
        84.9%
        34%
        70 bp
        7.6
        SRX7122765
        72.1%
        5.1
        91.2%
        6.5
        0.6%
        80.0%
        34%
        70 bp
        7.1
        SRX7122766
        73.9%
        5.8
        94.6%
        7.5
        0.0%
        83.6%
        34%
        70 bp
        7.9
        SRX7122767
        74.5%
        5.3
        94.1%
        6.7
        0.3%
        84.8%
        35%
        70 bp
        7.1
        SRX7122768
        76.7%
        6.2
        95.2%
        7.7
        0.2%
        83.2%
        34%
        70 bp
        8.1
        SRX7122769
        74.9%
        5.6
        94.2%
        7.0
        0.3%
        84.6%
        35%
        70 bp
        7.5
        SRX7122770
        94.1%
        97.5
        3.1%
        92.4%
        48%
        50 bp
        103.6
        SRX7122771
        14.7%
        11.0
        96.0%
        71.7
        2.4%
        93.9%
        48%
        50 bp
        74.6
        SRX7122772
        15.2%
        8.0
        96.6%
        50.9
        2.3%
        93.9%
        49%
        50 bp
        52.6
        SRX7711426
        0.8%
        0.6
        8.4%
        5.7
        4.0%
        94.2%
        56%
        49 bp
        67.6
        SRX7711427
        1.2%
        0.8
        13.7%
        9.9
        3.0%
        95.6%
        55%
        50 bp
        72.4
        SRX7711428
        1.7%
        1.3
        15.8%
        11.8
        2.8%
        95.4%
        55%
        50 bp
        75.2
        SRX7711429
        0.1%
        0.0
        0.9%
        0.6
        2.8%
        95.8%
        59%
        50 bp
        61.8
        SRX7711430
        0.0%
        0.0
        0.7%
        0.5
        3.1%
        95.9%
        59%
        50 bp
        70.3
        SRX7711431
        0.0%
        0.0
        0.7%
        0.7
        3.7%
        95.6%
        57%
        49 bp
        92.4
        SRX7711432
        71.7%
        7.9
        90.3%
        10.0
        1.3%
        68.1%
        36%
        73 bp
        11.0
        SRX7711433
        76.3%
        7.5
        92.9%
        9.2
        1.3%
        65.3%
        35%
        73 bp
        9.9
        SRX7711434
        59.3%
        8.9
        79.1%
        11.8
        2.1%
        65.5%
        36%
        73 bp
        15.0
        SRX7711435
        59.1%
        8.0
        81.2%
        10.9
        1.8%
        64.7%
        35%
        73 bp
        13.5
        SRX7711436
        71.7%
        17.2
        90.6%
        21.7
        1.5%
        70.8%
        35%
        73 bp
        24.0
        SRX7711437
        73.8%
        14.2
        92.0%
        17.7
        1.3%
        70.2%
        35%
        73 bp
        19.3
        SRX832419
        62.4%
        11.2
        85.1%
        15.3
        1.4%
        74.0%
        36%
        73 bp
        18.0
        SRX832420
        64.6%
        10.5
        87.2%
        14.2
        1.6%
        67.1%
        34%
        73 bp
        16.3
        SRX832421
        71.4%
        14.2
        92.5%
        18.4
        1.3%
        71.1%
        34%
        73 bp
        19.9
        SRX832422
        74.7%
        20.6
        93.3%
        25.7
        1.3%
        72.7%
        34%
        73 bp
        27.5
        SRX8640552
        66.1%
        14.4
        88.9%
        19.3
        1.4%
        69.6%
        34%
        73 bp
        21.7
        SRX8640553
        61.3%
        6.0
        80.4%
        7.9
        2.1%
        60.0%
        36%
        73 bp
        9.9
        SRX8640554
        11.0%
        7.4
        15.1%
        10.2
        1.2%
        73.7%
        55%
        73 bp
        67.5
        SRX8640555
        36.9%
        21.0
        47.1%
        26.9
        1.1%
        75.2%
        46%
        73 bp
        57.1
        SRX8640556
        16.5%
        5.1
        22.0%
        6.8
        1.1%
        70.0%
        54%
        73 bp
        30.7
        SRX8640557
        3.9%
        1.5
        5.1%
        2.0
        1.1%
        71.7%
        56%
        73 bp
        38.8
        SRX8640558
        4.8%
        2.1
        7.1%
        3.1
        1.0%
        73.7%
        58%
        74 bp
        43.7
        SRX8640559
        1.5%
        0.6
        1.9%
        0.8
        1.0%
        67.8%
        43%
        74 bp
        39.9
        SRX8783276
        2.4%
        1.1
        3.0%
        1.4
        1.0%
        66.4%
        42%
        74 bp
        46.5
        SRX8817788
        4.6%
        1.5
        5.8%
        1.9
        1.3%
        73.3%
        58%
        73 bp
        33.1
        SRX8817789
        0.4%
        0.2
        0.7%
        0.4
        0.9%
        67.4%
        54%
        74 bp
        49.7
        SRX8817790
        14.7%
        9.9
        18.2%
        12.3
        1.0%
        73.1%
        54%
        74 bp
        67.2
        SRX8817791
        2.1%
        1.2
        2.6%
        1.5
        1.1%
        73.9%
        58%
        73 bp
        56.9
        SRX8817798
        5.4%
        2.4
        7.2%
        3.2
        1.3%
        73.1%
        53%
        73 bp
        44.4
        SRX8817799
        25.6%
        2.4
        91.8%
        8.6
        1.1%
        81.3%
        42%
        48 bp
        9.3
        SRX9368291
        16.6%
        7.3
        97.5%
        42.7
        0.9%
        91.0%
        45%
        47 bp
        43.8
        SRX9368292
        41.1%
        23.2
        97.9%
        55.3
        0.9%
        86.1%
        42%
        48 bp
        56.5
        SRX9368293
        25.5%
        2.4
        91.6%
        8.6
        10.8%
        80.8%
        42%
        48 bp
        9.4
        SRX9368294
        16.6%
        7.3
        97.5%
        42.7
        7.7%
        90.6%
        46%
        48 bp
        43.8
        SRX9368295
        41.1%
        23.2
        97.8%
        55.3
        6.1%
        85.5%
        43%
        48 bp
        56.5
        SRX9368296
        25.5%
        2.4
        91.6%
        8.6
        10.8%
        80.8%
        42%
        48 bp
        9.4
        SRX9368297
        16.6%
        7.3
        97.5%
        42.7
        7.7%
        90.6%
        46%
        48 bp
        43.8
        SRX9368298
        76.9%
        10.3
        97.8%
        13.1
        0.9%
        88.3%
        35%
        50 bp
        13.4
        SRX9528673
        76.1%
        8.8
        97.6%
        11.3
        0.9%
        87.8%
        34%
        50 bp
        11.6
        SRX9528674
        77.8%
        11.4
        97.8%
        14.4
        0.9%
        88.4%
        35%
        50 bp
        14.7
        SRX9633997
        74.9%
        9.0
        97.8%
        11.8
        0.9%
        88.2%
        34%
        50 bp
        12.1
        SRX9633998
        77.7%
        7.2
        97.9%
        9.1
        0.9%
        87.0%
        35%
        50 bp
        9.3
        SRX9633999
        78.8%
        10.6
        98.0%
        13.2
        0.9%
        88.8%
        35%
        50 bp
        13.5
        SRX9634000
        41.1%
        23.2
        97.8%
        55.3
        6.1%
        85.5%
        43%
        48 bp
        56.5
        SRX9634001
        25.5%
        2.4
        91.6%
        8.6
        10.8%
        80.8%
        42%
        48 bp
        9.4
        SRX9634002
        16.6%
        7.3
        97.5%
        42.7
        7.7%
        90.6%
        46%
        48 bp
        43.8
        SRX9634003
        41.1%
        23.2
        97.8%
        55.3
        6.1%
        85.5%
        43%
        48 bp
        56.5
        SRX9634004
        80.9%
        6.6
        96.0%
        7.9
        1.8%
        81.8%
        36%
        40 bp
        8.2
        SRX9634005
        80.2%
        6.8
        95.8%
        8.1
        1.8%
        81.6%
        36%
        40 bp
        8.4
        SRX9634006
        79.1%
        5.9
        96.2%
        7.1
        1.9%
        81.5%
        35%
        40 bp
        7.4
        SRX9634007
        80.3%
        6.4
        96.4%
        7.7
        1.1%
        82.3%
        35%
        40 bp
        8.0
        SRX9634009
        3.0%
        2.3
        3.8%
        2.8
        0.8%
        60.1%
        44%
        149 bp
        75.1
        SRX9634010
        0.5%
        0.2
        0.7%
        0.2
        0.7%
        54.9%
        50%
        150 bp
        33.8
        SRX9634011
        0.8%
        0.4
        1.0%
        0.5
        0.7%
        57.9%
        48%
        150 bp
        53.4
        SRX9634012
        0.5%
        0.2
        0.6%
        0.3
        0.6%
        56.0%
        50%
        149 bp
        51.6
        SRX9634015
        0.6%
        0.3
        0.7%
        0.4
        0.7%
        55.6%
        48%
        150 bp
        51.0
        SRX9634016
        52.0%
        18.2
        55.8%
        19.6
        1.2%
        93.1%
        39%
        150 bp
        35.1
        SRX9634017
        40.3%
        12.0
        45.9%
        13.7
        1.2%
        92.2%
        39%
        150 bp
        29.8
        SRX9634018
        38.0%
        12.3
        43.2%
        14.0
        1.3%
        91.2%
        40%
        149 bp
        32.5
        SRX9634019
        42.7%
        6.7
        60.1%
        9.4
        0.4%
        86.3%
        44%
        69 bp
        15.7
        SRX9634020
        37.5%
        5.7
        58.1%
        8.8
        0.7%
        87.1%
        44%
        69 bp
        15.1
        SRX965931
        35.3%
        5.5
        58.1%
        9.0
        0.7%
        81.8%
        44%
        69 bp
        15.6

        featureCounts

        Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Bowtie 1

        Bowtie 1 is an ultrafast, memory-efficient short read aligner.

        This plot shows the number of reads aligning to the reference in different ways.

        There are 3 possible types of alignment: * Aligned: Read has only one occurence in the reference genome. * Multimapped: Read has multiple occurence. * Not aligned: Read has no occurence.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        RSeQC

        RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput RNA-seq data.

        Infer experiment

        Infer experiment counts the percentage of reads and read pairs that match the strandedness of overlapping transcripts. It can be used to infer whether RNA-seq library preps are stranded (sense or antisense).

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Cutadapt

        Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

        Filtered Reads

        This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Trimmed Sequence Lengths (3')

        This plot shows the number of reads with certain lengths of adapter trimmed for the 3' end.

        Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

        See the cutadapt documentation for more information on how these numbers are generated.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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